Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing

Abstract

BackgroundThe pure culture of prokaryotes remains essential to elucidating the role of these organisms. Scientists have reasoned that hard to cultivate microorganisms might grow in pure culture if provided with the chemical components of their natural environment. However, most microbial species in the biosphere that would otherwise be “culturable” may fail to grow because of their growth state in nature, such as dormancy. That means even if scientist would provide microorganisms with the natural environment, such dormant microorganisms probably still remain in a dormant state.ResultsWe constructed an enrichment culture system for high-efficiency isolation of uncultured strains from marine sediment. Degree of enrichment analysis, dormant and active taxa calculation, viable but non-culturable bacteria resuscitation analysis, combined with metatranscriptomic and comparative genomic analyses of the interactions between microbial communications during enrichment culture showed that the so-called enrichment method could culture the “uncultured” not only through enriching the abundance of “uncultured,” but also through the resuscitation mechanism. In addition, the enrichment culture was a complicated mixed culture system, which contains the competition, cooperation, or coordination among bacterial communities, compared with pure cultures.ConclusionsConsidering that cultivation techniques must evolve further—from axenic to mixed cultures—for us to fully understand the microbial world, we should redevelop an understanding of the classic enrichment culture method. Enrichment culture methods can be developed and used to construct a model for analyzing mixed cultures and exploring microbial dark matter. This study provides a new train of thought to mining marine microbial dark matter based on mixed cultures.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0613-2) contains supplementary material, which is available to authorized users.

Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments

“…Bradymonabacteria are e cient predators of diverse prey bacteria In total, 9 strains of bacteria in the novel order Bradymonadales were isolated using the enrichment culture method [22]. Among these strains, eight strains were isolated from costal sediment sampled in Weihai, China, while strain YN101 was isolated from a Gaodao saltern (36°54'N, 122°14'E) in Weihai, China.…”

Maribacter algarum sp. nov., a new member of the family Flavobacteriaceae isolated from the red alga Gelidium amansii

“…The authors declare that there are no conflicts of interest. five reasons to publish your next article with a Microbiology Society journal 1. The Microbiology Society is a not-for-profit organization.…”

“…The oceans contain inestimable biological resources, of which microbes are a significant portion [1]. Bacteria in the Bacteroidetes can be found in diverse marine environments and the family Flavobacteriaceae is one of the most important components of this phylum.…”

Mesohalobacter halotolerans gen. nov., sp. nov., isolated from a marine solar saltern

“…In recent years, researchers have paid more and more attention to studies of marine bacterial resources and committed to the development and utilization of marine microbial resources [11]. Genomics has become a promising methodology among prokaryotes which allows the continuation of our tradition of natural classification and the use of it to infer phylogenetic relationships.…”